All the various HTML templates used in your projects can be edited directly in the Configuration section of your project where they are stored. Help+Manual has an integrated HTML code editor with syntax highlighting, search and replace and spell checking.
Nowadays you will almost always choose an HTML skin to publish your project to WebHelp or HTML Help/CHM. A skin is a special kind of Help+Manual project without topics that only stores your HTML templates and all the settings relevant for HTML output to these two formats. When you choose a skin, the templates and settings in the skin completely replace those in your project.
Normally, a skin is pre-designed and you don't need to change anything. However, if you do want to change something, you must do all your editing in the .hmskin skin file. Editing in your Help+Manual project won't have any effect because those templates and settings are not used.
To edit a skin, make a copy of the .hmskin skin file in your project folder and then open it in Help+Manual by selecting .hmskin as the file type to open in the Open dialog. All the templates and settings are in the same places as in a normal Help+Manual project.
Exception: HTML Export Options
The HTML Export Options section is not stored in skins and needs to be edited in your project.
You must be familiar with manual HTML coding to edit the HTML templates yourself. Your code is also entirely your own responsibility – it is not syntax-checked in any way by Help+Manual. Only delete or change code in the standard templates if you really understand what you are doing, otherwise you may experience unexpected errors and malfunctions in your output!
When making code changes it is good practice to publish regularly to test the results of your changes, otherwise it can be difficult to localize and identify the changes that are causing a specific problem.
Help Windows (Reference)